Trollius europaeus
Globeflower
Info
| NCBI taxon id: | 212754 NCBI; ENA; GoaT |
|---|---|
| Order: | Ranunculales |
| Family: | Ranunculaceae |
| NCBI lineage: | Eukaryota;Viridiplantae;Streptophyta;Embryophyta;Tracheophyta;Spermatophyta;Magnoliopsida;Ranunculales;Ranunculaceae;Ranunculoideae;Adonideae;Trollius; |
| GoaT genome size (M): | 4,870 (direct) |
| GoaT asm span (M): | 604 (ancestor) |
| GoaT chr no.: | 16 (direct) |
| GoaT haploid no.: | 9 (direct) |
| GoaT ploidy: | 16 (ancestor) |
| ToLID prefix: | dmTroEuro |
Specimens
Below is information about specimens collected for this species retrieved from the Sample Tracking System (STS).
tolid | specimen_id | gal | sex | organism_part | biosample | biospecimen |
|---|---|---|---|---|---|---|
| dmTroEuro1 | EDTOL00059 | ROYAL BOTANIC GARDEN EDINBURGH | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA7536048 | SAMEA7535972 |
| dmTroEuro1 | EDTOL00059 | ROYAL BOTANIC GARDEN EDINBURGH | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA8596954 | SAMEA7535972 |
| dmTroEuro2 | EDTOL04728 | ROYAL BOTANIC GARDEN EDINBURGH | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA111431705 | SAMEA111431630 |
| dmTroEuro2 | EDTOL04728 | ROYAL BOTANIC GARDEN EDINBURGH | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA111431703 | SAMEA111431630 |
| dmTroEuro2 | EDTOL04728 | ROYAL BOTANIC GARDEN EDINBURGH | HERMAPHRODITE_MONOECIOUS | LEAF | SAMEA111431706 | SAMEA111431630 |
Spectra estimates
Below are estimates of genome size, repeat size, heterozygosity based on k-mer specta analysis with GenomeScope2.
source | specimen | k-mer | k-cov | haploid size | repeat (%) | heterozygosity (%) | model fit (%) | model error (%) | histogram |
|---|---|---|---|---|---|---|---|---|---|
| pacbio | dmTroEuro1 | 31 | 35.79 | 206,583,358 | 88.49 | 3.40 | 87.29 | 2.30 |   histogram.txt |
| 10x | dmTroEuro1 | 31 | 22.35 | 4,370,535,219 | 64.51 | 0.93 | 97.84 | 0.38 |   histogram.txt |
| pacbio | dmTroEuro2 | 31 | 20.11 | 1,831,486,421 | 70.43 | 11.58 | 84.23 | 0.61 |   histogram.txt |
| hic-arima2 | dmTroEuro2 | 31 | 4.568 | 74,395,973,052 | 0.00 | 100.00 | 11.08 | 0.18 |   histogram.txt |
Sequence data
PacBio run data
Below are stats for each PacBio seqeuncing run collected for this species.
pipeline | specimen | date | run id | movie | well | tag | yield | N50 | sample accession | run accession | barcode |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PacBio - HiFi | dmTroEuro1 | 2021-07-03 | 84018 | m64178e_210703_234946 | B01 | 1010 | 2,244,654,585 | 10,686 | SAMEA8596954 | ||
| PacBio - HiFi | dmTroEuro2 | 2023-01-14 | TRACTION-RUN-409 | m64230e_230114_223345 | C01 | 1002 | 15,112,594,830 | 16,453 | SAMEA111431706 | ||
| PacBio - HiFi | dmTroEuro2 | 2023-06-14 | TRACTION-RUN-629 | m84047_230614_145028_s1 | A01 | 2020 | 12,814,279,081 | 14,941 | SAMEA111431705 | ||
| PacBio - HiFi | dmTroEuro1 | 2023-07-19 | TRACTION-RUN-703 | m64221e_230719_142445 | A01 | 2035 | 28,258,683,195 | 15,615 | SAMEA7536048 | ||
| PacBio - HiFi | dmTroEuro2 | 2024-02-07 | TRACTION-RUN-1113 | m84098_240207_144339_s1 | C01 | 2001 | 60,564,399,737 | 10,212 | SAMEA111431705 | ||
| PacBio - HiFi | dmTroEuro2 | 2024-06-20 | TRACTION-RUN-1339 | m84098_240620_121914_s4 | D01 | 2008 | 935,964,931 | 9,750 | SAMEA111431703 |
ONT run data
Below are stats for each ONT seqeuncing run collected for this species.
pipeline | specimen | date | run id | flowcell | type | yield | N50 | sample accession | report |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Illumina run data
Below are stats for each Illumina run collected for this species. Click on a row to see associated plots from samtools stats.
pipeline | specimen | date | run id | read pairs | yield | sample accession | run accession | run status | barcode |
|---|---|---|---|---|---|---|---|---|---|
| Chromium genome | dmTroEuro1 | 2021-07-28 | 39212_4#23 | 342,107,480 | 51,658,229,480 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-30 | 39381_4#3 | 220,076,812 | 33,231,598,612 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-30 | 39381_4#4 | 293,057,028 | 44,251,611,228 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-30 | 39381_4#1 | 219,132,754 | 33,089,045,854 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-28 | 39212_4#22 | 189,630,316 | 28,634,177,716 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-28 | 39212_4#24 | 226,103,732 | 34,141,663,532 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-30 | 39381_4#2 | 251,096,324 | 37,915,544,924 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Chromium genome | dmTroEuro1 | 2021-07-28 | 39212_4#21 | 259,047,612 | 39,116,189,412 | SAMEA8596954 | qc complete | Trollius europaeus (1.00) | |
| Hi-C - Arima v2 | dmTroEuro2 | 2023-03-08 | 46852_1#1 | 5,943,438,018 | 897,459,140,718 | SAMEA111431706 | qc complete | Trollius europaeus (1.00) |
Cobionts
Below are results from a screen of the PacBio data using Mash screen against RefSeq assemblies. Only results with identity over 90% are displayed.
identity | info |
|---|---|
| 0.968984 | [15 seqs] NZ_LMKN01000001.1 Sphingomonas sp. Leaf20 contig_1, whole genome shotgun sequence [...] |
| 0.94619 | [17 seqs] NZ_LMPQ01000001.1 Frigoribacterium sp. Leaf186 contig_1, whole genome shotgun sequence [...] |
| 0.946046 | [151 seqs] NZ_JICM01000001.1 Acinetobacter sp. ETR1 contig_1, whole genome shotgun sequence [...] |
| 0.938887 | [14 seqs] NZ_LMKX01000001.1 Sphingomonas sp. Leaf28 contig_1, whole genome shotgun sequence [...] |
| 0.93855 | [15 seqs] NZ_LMKW01000001.1 Sphingomonas sp. Leaf230 contig_1, whole genome shotgun sequence [...] |
| 0.930032 | [15 seqs] NZ_LMKN01000001.1 Sphingomonas sp. Leaf20 contig_1, whole genome shotgun sequence [...] |
| 0.924653 | [22 seqs] NZ_LMOG01000001.1 Xanthomonas sp. Leaf131 contig_1, whole genome shotgun sequence [...] |
| 0.923498 | NC_018417.1 Candidatus Carsonella ruddii HT isolate Thao2000, complete genome |
| 0.922073 | [6 seqs] NZ_LMOX01000001.1 Frigoribacterium sp. Leaf164 contig_1, whole genome shotgun sequence [...] |
| 0.921343 | [12 seqs] NZ_LMKB01000001.1 Frigoribacterium sp. Leaf8 contig_1, whole genome shotgun sequence [...] |
Species composition by small subunit (SSU) presence in the assembly with MarkerScan.
specimen | contig | SSU length | attributed taxonomy by SSU |
|---|---|---|---|
| No matching records found | |||
MarkerScan cobiont assembly by read separation based on observed families (see above). These reads are both aligned to the assembly and independently re-assembled. The quality of these assemblies is assessed by their completeness according to BUSCO, their span and the number of reads they encompass. For more information here.
specimen | family | classified reads | original assembly | re-assembly | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
count | (%) | BUSCO | BUSCO | contigs | contig length | number of reads | BUSCO | contigs | contig length | number of reads | ||
| No matching records found | ||||||||||||
Visualisation of a classification of the PacBio reads using a variation autoencoder on the k-mer counts.
specimen | visualisation |
|---|---|
| dmTroEuro1 |    |
Canonical tetranucleotide counts for each contig or scaffold reduced to two dimensions with UMAP to allow visualisation.
Features (colours represent quantile bins):
- Hexamer: Estimated coding density (expected to be higher in microbes than in animals).
- FastK: The median number of times each 60-mer in the sequence occures across the whole assembly (illustrates repetitiveness)
- Unique_15mers: Number of unique 15-mers per base pair (illustrates sequence diversity)
- Is_Connected: Presence of at least one Hi-C connection to another scaffold (absence of connections can indicate contamination)
- Connections_Base: Number of Hi-C connections per base pair
Assemblies
In-progress assembly QC.
specimen | asm | date | contig N50 | contigs | scaffold N50 | scaffolds | length | BUSCO | merqury |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
Organelles
In-progress organelle results from MitoHiFi or Oatk.
specimen | asm | organelle | date | length | genes | frameshifts | is circular | seqs | reference |
|---|---|---|---|---|---|---|---|---|---|
| No matching records found | |||||||||
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